Phage display has become a powerful method for screening populations of peptide or polypeptides, mutated proteins, and cDNAs for members that have affinity to target molecules of interest. It is possible to generate many different recombinants from which one or more clones can be selected with affinity to antigens, antibodies, cell surface receptors, protein chaperones, DNA, metal ions, etc. Screening libraries are versatile because the displayed elements are expressed on the surface of the virus as capsid-fusion proteins. The most important consequence of this arrangement is that there is a physical linkage between phenotype and genotype. There are several other advantages as well: 1) virus particles which have been isolated from libraries by affinity selection can be regenerated by simple bacterial infection and 2) the primary structure of the displayed binding peptide or protein can be easily deduced by DNA sequencing of the cloned segment in the viral genome.
Synthetic oligonucleotides that are fixed in length, but with multiple unspecified codons can be cloned into genes III, VI, or VIII of bacteriophage Ml 3 where they are expressed on the capsid fusion protein. The libraries, often referred to as random peptide libraries, can be screened for binding to target molecules of interest.
Most vital cellular processes are regulated by the transmission of signals wherein such signal transduction is likely mediated by protein-protein interactions involving modular domains within the signaling proteins.
Methods for isolating partner proteins involved in protein-protein interactions have generally focused on finding a ligand to a characterized protein. Such approaches have included using anti-idiotypic antibodies that mimic the known protein to screen cDNA expression libraries for a binding ligand (Jerne, 1974, Ann. Immunol. (Inst. Pasteur) 125c:373-389; Sudol, 1994, Oncogene 9:2145-2152). Skolnick et al. (1991, Cell 65:83-90) isolated a binding partner for PI3-kinase by screening a cDNA expression library with the 32P-labeled tyrosine phosphorylated carboxyl terminus of the epidermal growth factor receptor (EGFR). While current methods provide for the identification and isolation of a peptides having an intermolecular interaction with a target of interest, functional analysis of the screening steps is currently lacking.